Integration of Generative Protein Design with Synthetic Porphyrin Assembly: Metal-Responsive Cyclic Assembly of a...

De novo protein design has been used to create functional protein assemblies, but its reliance on standard amino acids limits the integration of synthetic supramolecular strategies for precise control of molecular assemblies. Herein, an artificial protein assembly that integrates synthetic supramolecular design with de novo protein engineering is presented. Focusing on unit and connection rigidity, the Bi-Porphyrin Acquisition Designer protein (BiPAD), which captures two synthetic porphyrin molecules via state-of-the-art generative protein design to fuse α/β-folded porphyrin-binding motifs, is designed and created. BiPADs captures rigid porphyrins, each bearing an additional metal coordination site, resulting in a metal-responsive cyclic assembly with the intended structure. Furthermore, high-speed atomic force microscopy reveals dynamic structural changes in the BiPAD assembly. This work expands the designability of artificial protein assemblies, paving the way for the synergistic design of functional systems through the integration of protein engineering and synthetic chemistry.